Genetic Variant NM_178819.4:c.1262+495A>G (chr8-41619472-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_178819.4(GPAT4):c.1262+495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 173,204 control chromosomes in the GnomAD database, including 602 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.080 ( 550 hom., cov: 33)

Exomes 𝑓: 0.061 ( 52 hom. )

Consequence

GPAT4
NM_178819.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.131

Publications

4 publications found

Variant links:

Genes affected

GPAT4 (HGNC:20880): (glycerol-3-phosphate acyltransferase 4) Lysophosphatidic acid acyltransferases (EC 2.3.1.51) catalyze the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA). LPA and PA are involved in signal transduction and lipid biosynthesis.[supplied by OMIM, Apr 2004]

GPAT4 links:

ENSG00000264578 (HGNC:):

ENSG00000264578 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPAT4	NM_178819.4 link	c.1262+495A>G		intron_variant	Intron 12 of 12	ENST00000396987.7	NP_848934.1	Q86UL3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GPAT4	ENST00000396987.7 link	c.1262+495A>G	intron_variant	Intron 12 of 12	1	NM_178819.4	ENSP00000380184.3	Q86UL3
GPAT4	ENST00000518628.1 link	n.561+121A>G	intron_variant	Intron 2 of 2	3
GPAT4	ENST00000521349.1 link	n.361+495A>G	intron_variant	Intron 2 of 2	2
ENSG00000264578	ENST00000581909.1 link	n.546+1485T>C	intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.0805

AC:

12244

AN:

152142

Hom.:

549

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0901

Gnomad AMI

AF:

0.0341

Gnomad AMR

AF:

0.0909

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0455

Gnomad FIN

AF:

0.0402

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0845

Gnomad OTH

AF:

0.104

GnomAD4 exome

AF:

0.0606

AC:

1269

AN:

20944

Hom.:

AF XY:

0.0612

AC XY:

662

AN XY:

10822

show subpopulations

African (AFR)

AF:

0.100

AC:

AN:

518

American (AMR)

AF:

0.0640

AC:

202

AN:

3156

Ashkenazi Jewish (ASJ)

AF:

0.0710

AC:

AN:

324

East Asian (EAS)

AF:

0.00

AC:

AN:

1494

South Asian (SAS)

AF:

0.0373

AC:

AN:

2522

European-Finnish (FIN)

AF:

0.0289

AC:

AN:

554

Middle Eastern (MID)

AF:

0.118

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0712

AC:

811

AN:

11390

Other (OTH)

AF:

0.0704

AC:

AN:

952

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

112

167

223

279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0805

AC:

12250

AN:

152260

Hom.:

550

Cov.:

AF XY:

0.0790

AC XY:

5881

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.0901

AC:

3740

AN:

41532

American (AMR)

AF:

0.0907

AC:

1387

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

431

AN:

3472

East Asian (EAS)

AF:

0.000578

AC:

AN:

5188

South Asian (SAS)

AF:

0.0460

AC:

222

AN:

4826

European-Finnish (FIN)

AF:

0.0402

AC:

427

AN:

10622

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0846

AC:

5751

AN:

68014

Other (OTH)

AF:

0.103

AC:

217

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

583

1165

1748

2330

2913

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0846

Hom.:

713

Bravo

AF:

0.0841

Asia WGS

AF:

0.0210

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.4

(source)

DANN

Benign

0.26

PhyloP100

0.13

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over